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Single Cell Portal @SingleCellBroad

Web app for single-cell genomics data, reducing barriers and accelerating research. Built at the Broad Institute.

Joined November 2021
  • Tweets 66
  • Following 4
  • Followers 95
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Single Cell Portal@SingleCellBroad
17 Jul 2023
We wrote a white paper! In it, we highlight how SCP accelerates single-cell omics research by making it easy to share and explore data. Read it at broad.io/scpPaper
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How does gene expression relate to disease mechanisms and gene regulatory networks?  New pathway search and visualization features in Single Cell Portal give insight! Learn more: broad.io/scp-pathways #SingleCell #Biology #GeneRegulatoryNetwork
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Did you know Single Cell Portal comprehensively validates #singlecell data *before* you upload?  Authors learn of issues in < 10 seconds -- not minutes or hours -- with clear, actionable messages. Click "Create study" at singlecell.broadinstitute.or… to try SCP's fast, easy upload. ⚡️
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Each month, over 22K users from > 160 organizations use Single Cell Portal.  Increase the impact of your science by creating a study at singlecell.broadinstitute.or…!
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Single Cell Portal now supports exploring #multiome ATAC data!  Simply upload your #singlecell ATAC fragment data, then visualize and filter it in a genome browser.  Learn more about comparing chromatin accessibility and gene expression: singlecell.broadinstitute.or…
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Check out three new #singlecell studies on molecular cartography in mouse intestine by Toufic Mayassi, Chenhao Li and colleagues in Xavier lab @broadinstitute: singlecell.broadinstitute.or…, singlecell.broadinstitute.or…, singlecell.broadinstitute.or…
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Single Cell Portal retweeted
Margaret Schroeder@meschro
13 Oct 2024
Very excited to share our pre-print and my thesis work on the postnatal development of astrocyte regional heterogeneity, which includes an integrated dataset of >1.4 million single nuclei transcriptomes in mouse and marmoset brains (now available online)! biorxiv.org/content/10.1101/…

Astrocyte regional specialization is shaped by postnatal development

Astrocytes are an abundant class of glial cells with critical roles in neural circuit assembly and function. Though many studies have uncovered significant molecular distinctions between astrocytes...

biorxiv.org
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How might AI ease the burden of cell type annotation? SCP tried out Cellarium Cell Annotation Service (CAS) on a 10x PBMC dataset to find out. Explore our demo (CAS) study: singlecell.broadinstitute.or…

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Read more at broad.io/scp-cas-announcemen… and give us feedback on how you would use a cell annotation service at broad.io/scp-cas-survey
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Exploratory DE results are now available for new AnnData studies! Create a study, upload your AnnData file, then find and visualize differentially expressed genes. singlecell.broadinstitute.or…
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Since 5/2020, Single Cell Portal has had: - 582K active users (currently 215K / year, up 42% YoY) - 2.3M page views - 3.7M user searches for studies and genes And we host 76M cells: 48M public, 28M private. Explore, upload, share! singlecell.broadinstitute.or…
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Differential Expression data in Single Cell portal can now be filtered for more focused exploration. broad.io/DiffExpAd2
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Quickly and easily view post-filtering DEGs in a dot plot. broad.io/DiffExpUpdate
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As a study owner, you can upload your differential expression data for visualization in Single Cell Portal broad.io/DiffExpUpload
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Want to explore single cell studies, or publish your own? Check out youtu.be/lclq_6olqqc for a recent overview of Single Cell Portal: search, differential expression, cell filtering, spatial transcriptomics, study creation, public vs. private studies, and more!

2024 Single Cell Portal overview and demo

In this overview, we try out key features in Single Cell Portal (ht...

youtube.com
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Filter plotted cells to refine visualizations in Single Cell Portal! Drill down to visualize gene expression for one or more experimental variables. Read about the feature (broad.io/scp-filter-plot-FA) or dive into the documentation (broad.io/scp-filter-plot-doc…).
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New feature alert: you can now upload AnnData files to power visualizations to Single Cell Portal! broad.io/h5adonscp (image from anndata.readthedocs.io/en/la…) 1/5
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If you’re interested in uploading AnnData to SCP, let us know by liking this tweet or by filling in this 2-minute survey: broad.io/h5adSurvey 4/5

Uploading AnnData files on Single Cell Portal

Let us know how we can make it easier to upload AnnData files (also called .h5ad) in this 5-minute survey.

docs.google.com
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And if you have questions or additional comments, drop us an email at scp-support@broadinstitute.zendesk.com 5/5
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